November 14, 2018

Today’s digest is about how dietary shifts and low gluten diet changes the intestinal microbiome, fecal microbiota transplant in intestinal disorders, characterization of the most abundant bacteriophage family in the human gut, and Raman spectroscopy based method for fast identification of antibiotic resistance bugs.

Human gut microbiome

Fecal microbiota transplantation for refractory immune checkpoint inhibitor-associated colitis – Yinghong Wang – Nature Medicine

A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults – Lea BS Hansen – Nature Communications

Resilience of human gut microbial communities for the long stay with multiple dietary shifts – Hong Liu – Gut

Microbiome and its relation to gestational diabetes – Ramon V. Cortez – Endocrine

Effect of bifidobacterium breve A-1 on anxiety and depressive symptoms in schizophrenia: A proof-of-concept study – Ryo Okubo – Journal of Affective Disorders

Fecal Akkermansia muciniphila Is Associated with Body Composition and Microbiota Diversity in Overweight and Obese Women with Breast Cancer Participating in a Presurgical Weight Loss Trial – Andrew D Fruge – Journal of the Academy of Nutrition and Dietetics

An Open-Labeled Study on Fecal Microbiota Transfer in Irritable Bowel Syndrome Patients Reveals Improvement in Abdominal Pain Associated with the Relative Abundance of Akkermansia Muciniphila – Cruz-Aguliar RM – Digestion

Animal experiments

Berberine alleviates insulin resistance by reducing peripheral branched-chain amino acids – Shi-Jun Yue – American Journal of Physiology Endocrinology and Metabolism

Air microbiome

A long-term survey unveils strong seasonal patterns in the airborne microbiome coupled to general and regional atmospheric circulations – Joan Cáliz – PNAS

Phages and viruses

ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis – Andrey N Shkoporov – Nature Communications

Techniques

Quantifying and comparing bacterial growth dynamics in multiple metagenomic samples – Yuan Gao – Nature Methods

Dynamic linear models guide design and analysis of microbiota studies within artificial human guts – Justin D Silverman – Microbiome

Microbes in the news

Chinese scientists develop novel instrument for rapid profiling of antimicrobial resistance – EurekaAlert

Microbes on the market

Chr. Hansen Receives Joint Innovation Fund Grant to Develop Next Generation Microbial Solutions for Agriculture – Microbiome times

Non-microbiology picks

Remission of Human Type 2 Diabetes Requires Decrease in Liver and Pancreas Fat Content but Is Dependent upon Capacity for β Cell Recovery – Roy Taylor – Cell Metabolism

 

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October 25, 2018

Roller coaster of fantastic articles today! Two sister articles from TEDDY cohort about development of the gut microbiota in early childhood and type-1 diabetes. Another article on association of the early gut microbiota with body mass index later in life in a Norwegian cohort. A multi-omics study of the rumen microbiota and insight into how human gut microbiota recovers following antibiotic exposure. And many more, keep reading…

Human gut microbiome

Recovery of gut microbiota of healthy adults following antibiotic exposure – Albert Palleja – Nature Microbiology

The human gut microbiome in early-onset type 1 diabetes from the TEDDY study – Tommi Vatanen – Nature

Temporal development of the gut microbiome in early childhood from the TEDDY study – Christopher J. Stewart – Nature

Gut Microbiota in the First 2 Years of Life and the Association with Body Mass Index at Age 12 in a Norwegian Birth Cohort – Maggie A. Stanislawski – mBio

Human gut microbe co-cultures have greater potential than monocultures for food waste remediation to commodity chemicals – Matthew A. Perisin – Scientific Reports

Animal experiments

Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem – Lindsey M. Solden – Nature Microbiology

A gut microbial factor modulates locomotor behaviour in Drosophila – Catherine E. Schretter – Nature

Dietary fibers inhibit obesity in mice, but host responses in the cecum and liver appear unrelated to fiber-specific changes in cecal bacterial taxonomic composition – Janice E. Drew – Scientific Reports

Plant, root, and soil microbiome

Existing Climate Change Will Lead to Pronounced Shifts in the Diversity of Soil Prokaryotes – Joshua Ladau – mSystems

Techniques

Intestinal barrier dysfunction orchestrates the onset of inflammatory host–microbiome cross-talk in a human gut inflammation-on-a-chip – Woojung Shin – PNAS

Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and whole rrn operon – Anna Cusco – BioRxiv

Microbes in the news

3 million common procedures in England could become ‘life threatening’ without antibiotics – CNN

Antibiotic plus probiotic combination may kill off superbugs – Medical News Today

Microbes on the market

Microbiotica Attracts Equity Investment from Seventure’s Health for Life Capital Fund – Microbiome Times

Rebiotix and Microbiome Insights Collaborate on a Microbiome IBD Tool for Clinical Development – Microbiome Times

APC Microbiome Ireland pool resources to lead maternity probiotic venture – Nutraingredients.com

Non-microbiology picks

How should autonomous vehicles be programmed? – ScienceDaily

October 18, 2018

Today’s digest covers articles on the potential of fecal microbiota transplant in obesity and Crohn’s disease, modeling approach to address interactions in simplified microbial community, news on antibiotic resistance and a gigantic single cell transcriptomics database encompassing twenty mouse organs!

General Microbiome

Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community – Kevin D’hoe – eLife

The role of the lung microbiota and the gut‐lung axis in respiratory infectious diseases – Alexia Dumas – Cellular Microbiology

Gut microbiota and obesity: An opportunity to alter obesity through Fecal Microbiota Transplant (FMT) – Patrick Lee – Diabetes Obesity and Metabolism

Human gut microbiome

Probiotic supplementation restores normal microbiota composition and function in antibiotic-treated and in caesarean-born infants – Katri Korpela – Microbiome

Diversified gut microbiota in newborns of mothers with gestational diabetes mellitus – Minglian Su – PlosOne

Gut dysbiosis with Bacilli dominance and accumulation of fermentation products precedes late-onset sepsis in preterm infants – S Graspeuntner – Clinical Infectious Diseases

The Safety of Fecal Microbiota Transplantation for Crohn’s Disease: Findings from A Long-Term Study – Honggang Wang – Advances in Therapy

Animal experiments

Effect of dietary Spirulina (Arthrospira) platensis on the growth performance, antioxidant enzyme activity, nutrient digestibility, cecal microflora, excreta noxious gas emission, and breast meat quality of broiler chickens – J H Park – Poultry Science

Water and extremophile microbiome

Differential incorporation of one-carbon substrates among microbial populations identified by stable isotope probing from the estuary to South China Sea – Wenchao Deng – Scientific Reports

Prokaryotic Diversity and Distribution in Different Habitats of an Alpine Rock Glacier-Pond System – I. Mania – Microbial Ecology

Community composition of nitrous oxide reducing bacteria investigated using a functional gene microarray – A. Jayakumar – Deep Sea Research Part II: Topical Studies in Oceanography

Built environment

Microbial and Metabolic Succession on Common Building Materials Under High Humidity Conditions – Simon Lax – BioRxiv

Bioinformatics/Techniques

Designing metabolic division of labor in microbial communities – Meghan Thommes – BioRxiv

Population heterogeneity in microbial bioprocesses: origin, analysis, mechanisms, and future perspectives – Anna-Lena Heins – Bioprocess and Biosystems Engineering

Hydrogenotrophic methanogens of the mammalian gut: functionally similar, thermodynamically different. A modelling approach – Rafael Munoz-Tamayo – BioRxiv

Microbes in the news

Most burger chains fail on annual antibiotics report card – CNN

Sales of antibiotics for use in food-producing animals drop across the EU – European Medicine Agencies News

Non-microbiology picks

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris – The Tabula Muris Consortium – Nature

September 26, 2018

Today’s mid-week short digest includes articles on integrating human genetics and the gut microbiome to find potent risk factors in cardiovascular disease; comparison of bariatric surgery techniques on the gut microbiota; transmission of antibiotic resistance genes from mothers to infants and importance of breastfeeding. News updates on growth prediction of human microbiome based diagnostics and first rapid test to determine Bifidobacteria in infant gut!

Human gut microbiome

Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome – Daria V. Zhernakova – Nature Genetics

Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements – Katariina Pärnänen – Nature Communications

Multidrug-resistant Gram-negative bacteria from patients, hospital environment and healthcare workers: a six-month cross-sectional study – Aline Fernanda Rodrigues Sereia – bioRxiv

Microbiota stability in healthy individuals after single-dose lactulose challenge – a randomized controlled study – Sandra Y Wotzkas – bioRxiv

Laparoscopic Roux-en-Y gastric bypass profoundly changes gut microbiota compared to laparoscopic sleeve gastrectomy: a metagenomic comparative analysis – William Farin – bioRxiv

Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health – Kathrin Beyer – PlosOne

Profiling of microorganism-binding serum antibody specificities in professional athletes – Rajna Minić – PlosOne

Animal experiments

Human Breast-Milk Feeding Enhances the Humoral and Cell-Mediated Immune Response in Neonatal Piglets – John J Miklavcic – The Journal of Nutrition

Glyphosate perturbs the gut microbiota of honey bees – Erick V. S. Motta – PNAS

Water and extremophile microbiome 

Microbiome profiling in extremely acidic soils affected by hydrothermal fluids: the case of Solfatara Crater (Campi Flegrei, southern Italy) – Crognale Simona – Fems Microbiology Ecology

Techniques

The Smallest Intestine (TSI) – a low volume in vitro model of the small intestine with increased throughput – T Cieplak – FEMS microbiology Letters

Microbes in the news

First-Ever Rapid Response Test for Levels of Bifidobacterium in Baby’s Gut Microbiome – Microbiome Times

Human Microbiome Market will Likely to expanding at a CAGR of 9.8% during the forecast period from 2018 to 2026 – Business Analyst

Puppies spread antibiotic-resistant infections to 118 people, CDC reports – CBS News

Non-microbiology picks

The best of intentions: Prenatal breastfeeding intentions and infant health – Kerri M. Raissian – SSM Population Health

 

September 20, 2018

Today’s digest presents reviews covering potential of microbiome in olfactory communication and oral-gut microbiome axis in rheumatoid arthritis; articles on association of human gut microbiome with different diseases; news on antibiotics and scientific data on personality types in humans.

General microbiome

Review: The Extended Genotype: Microbially Mediated Olfactory Communication – Alexandra J.R. Carthey – Trends in Ecology and Evolution

Talk to your gut: the oral-gut microbiome axis and its immunomodulatory role in the etiology of rheumatoid arthritis – Marines du Teil Espina – FEMS Microbiology Reviews

Commmentary: Regulating stool for microbiota transplantation – Pilar N Ossorio – Gut microbes

Proteomics and the microbiome: pitfalls and potential – Huafeng Lin – Expert Review of Proteomics

Pregnancy and early life

Postnatal exposure to household disinfectants, infant gut microbiota and subsequent risk of overweight in children – Mon H. Tun – Canadian Medical Association Journal

Human gut microbiome

Gut Microbiota Differs in Composition and Functionality Between Children With Type 1 Diabetes, MODY2, and Healthy Control Subjects: A Case-Control Study – Isabel Leiva-Gea – Diabetes Care

Analysis of gut microbiota profiles and microbe-disease associations in children with autism spectrum disorders in China – Mengxiang Zhang – Scientific Reports

Mucosal microbiota of intestinal polyps reveals putative biomarkers of colorectal cancer – Marta Mangifesta – Scientific Reports

Predicting recurrence of Clostridium difficile infection following encapsulated fecal microbiota transplantation – Christopher Staley – Microbiome

Could fecal phenylacetic and phenylpropionic acids be used as indicators of health status? – Isabel Gutiérrez-Díaz – Journal of Agricultural and Food Chemisty

Altered intestinal antibacterial gene expression response profile in irritable bowel syndrome is linked to bacterial composition and immune activation – Sean M. P. Bennet – Neurogastroenterology and Motility

Animal experiments

Melatonin reprogramming of gut microbiota improves lipid dysmetabolism in high fat diet-fed mice – Jie Yin – Journal of Pineal Research

Water and extremophile microbiome

Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake – Keith Arora-Williams – Microbiome

Probiotics/Prebiotics

The Impact of Probiotic Supplements on Cognitive Parameters in Euthymic Individuals with Bipolar Disorder: A Pilot Study – Eva Z Reininghaus – Neuropsychobiology

Microbes in the news

The case for expensive antibioticshttp://www.wired.com

Crucial antibiotics still used on US farms despite public health fear  The Guardian

Non-microbiology picks

A robust data-driven approach identifies four personality types across four large data sets – Martin Gerlach – Nature Human Behaviour

 

Article post

Microbiota depletion shifts colonocyte substrate utilization

In the fed state, glucose is the major fuel to most cell types in the body. In contrast, colonic epithelial cells or colonocytes utilize butyrate as their major energy source. Butyrate is one of the short chain fatty acids (SCFAs), a class of microbial metabolites produced by microbial fermentation of dietary fiber in gut. When the gut microbiota is depleted, such as in germ-free (GF) mice, butyrate levels along with other SCFAs decline prompting “starved” colonocytes to shift their substrate utilization to an alternative fuel, such as glucose.

Glucose undergo oxidative metabolism in cells to produce energy. In contrast, early ex vivo experiments studying substrate utilization in isolated colonocytes of rats using radioactive tracers revealed that about 80% of glucose is rather converted into lactate in colonocytes [1]. Later Donohoe et al., found that colonocytes from GF mice produce approx. 4 times higher lactate compared with conventionally raised mice through anaerobic glycolysis of glucose [2]. However, lactate production is not an energy rewarding process and yields only 2-4 ATP compared with 36 ATPs from oxidative phosphorylation of glucose. Thus, the authors concluded that despite the shift in substrate utilization, the colonocytes in the GF mice remain in energy insufficient state [2].

In the recent article published in Nature Communications by Zarrinpar et al. [3], where gut microbiota (and butyrate!) was depleted using multiple gavage of antibiotics over the course of 4 weeks. The authors found that cecum tissue uses glucose as an alternative fuel in the absence of butyrate, and that the expression levels of 8 out of 10 enzymes in glycolysis pathway were upregulated in cecum of antibiotic- compared with vehicle-treated mice. Finally, they speculate that due to shift in substrate utilization in cecum, gut becomes a glucose sink that could account for overall improvement in glucose metabolism in the antibiotic-treated mice [3].

Perhaps this speculation needs more careful investigation. It is true that colonocytes use butyrate as their primary fuel; however, butyrate is not synthesized in isolation. Gut microbiota produces SCFAs that include acetate, propionate and butyrate. It has been shown that colonocytes prefer other SCFA such as acetate over glucose [4] probably because anaerobic glycolysis of glucose does not yield enough energy. In the article by Zarrinpar et al., there was a trend towards reduction of acetate in antibiotic- compared with vehicle-treated mice, but it was not depleted to the same level as butyrate [3]. Secondly, shift in colonocyte substrate utilization from butyrate to glucose is also observed in inflammatory bowel disease and DSS colitis model. This is indicated to be due to alteration in butyrate uptake and thus colonocytes utilize glucose leading to high amount of lactate accumulation in cells [5]. However, patients with IBS are more prone to develop glucose intolerance than the healthy people.

Studying substrate utilization in cecum/colonocytes is complex. It is true that the isolated colonocytes do not reflect the in vivo scenario. However, transcriptomic data (showing increased expression of glycolytic enzymes in intestinal tissue of antibiotic-treated mice) probably needs to be backed with enzyme activity measurements and tracer studies to  understand its impact on overall metabolism.

1. Ardawi, M.S. and E.A. Newsholme, Fuel utilization in colonocytes of the rat. Biochem J, 1985. 231(3): p. 713-9.

2. Donohoe, D.R., et al., Microbial regulation of glucose metabolism and cell-cycle progression in mammalian colonocytes. PLoS One, 2012. 7(9): p. e46589.

3. Zarrinpar, A., et al., Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism. Nat Commun, 2018. 9(1): p. 2872.

4. Clausen, M.R. and P.B. Mortensen, Kinetic studies on the metabolism of short-chain fatty acids and glucose by isolated rat colonocytes. Gastroenterology, 1994. 106(2): p. 423-32.

5. Thibault, R., et al., Butyrate utilization by the colonic mucosa in inflammatory bowel diseases: a transport deficiency. Inflamm Bowel Dis, 2010. 16(4): p. 684-95.

December 21, 2017

Today’s digest features an original research article showing administration of Bifidobacterium may ameliorate toxicity of a a checkpoint blockade antibody in mice and a review on the concept of enterotypes in the human gut microbiome.

Events and jobs

Explorations in Data Analyses for Metagenomic Advances in Microbial Ecology (EDAMAME) workshop at Kellogg Biological Station 24-30 June 2018.

Human respiratory microbiome

Disordered oropharyngeal microbial communities in H7N9 patients with or without secondary bacterial lung infection – Emerging microbes & infections – Hai-feng Lu

Human gut microbiome

Review: Gut microbiota in 2017: Contribution of gut microbiota–host cooperation to drug efficacy – Nathalie M. Delzenne – Nature reviews gastroenterology & hepatology

Editorial : Are diets the answers to colon ills? Food, irritable bowel syndrome and the microbiome – Quigley Eamonn M.M.

Exposure to environmental microbiota explains persistent abdominal pain and irritable bowel syndrome after a major flood – NurFadhilah Yusof – Gut Pathogens

*Perspective : Enterotypes in the landscape of gut microbial community composition – Paul I. Costea – Nature Microbiology

Animal experiments

Evaluation of Probiotic Lactobacillus fermentum CCM 7421 Administration with Alginite in Dogs – Viola Strompfová – Probiotics and Antimicrobial Proteins

Bifidobacterium can mitigate intestinal immunopathology in the context of CTLA-4 blockade – Feng Wang – PNAS

Plant, root, and soil microbiome

Biogeography and ecological diversity patterns of rare and abundant bacteria in oil-contaminated soils – Shuo Jiao – Molecular ecology

Water and extremophile microbiome 

Bacterial Diversity and Biogeochemistry of Two Marine Shallow-Water Hydrothermal Systems off Dominica (Lesser Antilles) – Petra Pop Ristova – Frontiers in Microbiology

Temporal Dynamics of the Microbial Community Composition with a Focus on Toxic Cyanobacteria and Toxin Presence during Harmful Algal Blooms in Two South German Lakes – Pia I. Scherer – Frontiers in Microbiology

Probiotics / prebiotics

Galactooligosaccharide supplementation provides protection against Citrobacter rodentium-induced colitis without limiting pathogen burden – Hatem Kittana – Microbiology

Bifidobacteria and Their Molecular Communication with the Immune System – Lorena Ruiz – Frontiers in Microbiology

Phages and viruses

Toward Understanding Phage:Host Interactions in the Rumen; Complete Genome Sequences of Lytic Phages Infecting Rumen Bacteria – Rosalind A. Gilbert – Frontiers in Microbiology

Resolution of habitat-associated ecogenomic signatures in bacteriophage genomes and application to microbial source tracking – Lesley A. Ogilvie – The ISME Journal

Pre-print: Temperate phages as self-replicating weapons in bacterial competition – Xiang-Yi Li – bioRxiv

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Microbes in the news

Researchers Create Bacteria-Killing Steel Nanospikes

Are phages our best bet against antibiotic-resistant bacteria?

Bacteria Art

Science and Art Join Forces to Challenge our Anthropocentric Worldviews

Loyola Biology Professor Will Display Art At ARC Gallery

Anitha’s non-microbiology picks

Scientists discover entirely new material that cannot be explained by classical physics

Smothered jet may explain weird light from neutron star crash

Study of beetle flagellum offers possible way to improve medical devices